Question: How to retrieve 'conservation score' sequence?
10.4 years ago by
Guido Hooiveld • 2.4k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld • 2.4k wrote:
Hi, I have a list of putative transcription factor binding sites, and in order to continue with the most relevant ones for further analyses i would like to filter on 'conservation score' (the assumption is that conserved sequences are more likely to be functional than less/non conserved sequences). I have read on this, and found out that both ENSEMBL (GERP score) and UCSC Browser (multiz alignment) provide this info (although calculated using different algorithms). Moreover, in both genome browsers i can view the score. However, i don't know how to retrieve the score for a list of sequences... I was thinking/hoping that e.g. biomart could be used for this, but i could not find the appropriate filter. I am not familiar enough yet with UCSC to find a suitable way of doing this. Therefore, any pointer on how to best tackle this issue would be appreciated! TIA, Guido ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> email: firstname.lastname@example.org [[alternative HTML version deleted]]
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